User GuideΒΆ Introduction System Requirements Expert usage FreeSurfer Downstream Modules Want to know more? Intended Use References Acknowledgements Quick Start Singularity or Docker Google Colab Installation Linux MacOS Windows Examples Example 1: FastSurfer Singularity (or Apptainer) Example 2: FastSurfer Docker Example 3: Native FastSurfer on subjectX with parallel processing of hemis Example 4: FastSurfer on multiple subjects Example 5: Quick Segmentation Example 6: Running FastSurfer on a SLURM cluster via Singularity Output files Segmentation module Corpus Callosum module CerebNet module HypVINN module Surface module Longitudinal Processing Modules Corpus Callosum Pipeline Docker Support Pull FastSurfer from DockerHub Running the (official) Docker Image FastSurfer Docker Image Creation Build docker image with attestation and provenance Building for release Singularity Support Containerization Using Singularity (or Apptainer) Downloading the official FastSurfer image for Singularity Creating your own FastSurfer Singularity image Starting FastSurfer with from a Singularity image Common problems Best Practices Running FastSurfer as MacOS package Manual Edits What are Edits? What can be edited? Pipeline overview Possible Edits General process Bias field correction asegdkt_segfile Talairach registration White matter segmentation Pial surface placement Side effects of edits Guide for experienced FreeSurfer users What NOT to do Longitudinal Processing What is Longitudinal Processing? How to Run Your Data Single Time Point Cases Behind the Scenes Final Statistics References Security Policy Supported Versions Reporting a Vulnerability FastSurfer License Apache License Other Packages and Tools distributed or used with FastSurfer